6-106700598-G-C

Position:

• chr6-106700598-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.859 in 152,238 control chromosomes in the GnomAD database, including 56,295 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.86 (56295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130655 AN: 152120 Hom.: 56233 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.855

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.859 AC: 130777 AN: 152238 Hom.: 56295 Cov.: 32 AF XY: 0.859 AC XY: 63932 AN XY: 74426

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.857

Alfa AF: 0.855 Hom.: 2756

Bravo AF: 0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2798360; hg19: chr6-107148473;